update template

MS/MS.qmd

@@ -12,42 +12,46 @@ bibliography: [../BB/Ref.bib, ../BB/localRef.bib]
 csl: _extensions/inst/tex/elsevier-harvard.csl
 format:
   elsevier-html:
+    toc: true
     css: _extensions/inst/css/style.css
     keep-md: true
   epub: default
   docx:
     reference-doc: _extensions/inst/word/MS.docx
-  elsevier-pdf:
+  pdf:
-    keep-tex: false
+    # documentclass: article
+    latex-clean: false # to keep aux
+    citecolor: blue
+    colorlinks: true
+    number-sections: true
+    sansfont: "Gill Sans"
+    papersize: a4paper
+    sansfontoptions: 
+      - Color=39729E
+    mainfont: "Source Sans 3" #| Verdana (fontsize: 11pt) # Source Sans 3 | Times New Roman| Helvetica | PT Sans
+    monofont: "JetBrains Mono"
+    mathfont: "Cambria Math"
+    CJKmainfont: SimHei
+    fontsize: 12pt
     keep-md: false
-    include-in-header: "./_extensions/quarto-journals/elsevier/partials/revision.tex"
+    include-in-header: "./_extensions/inst/tex/header.tex"
-    latex-clean: false
     header-includes:
-      # - \usepackage{threeparttable}
       # - \usepackage{fontspec}
-      # - \usepackage{endfloat}
+      - \usepackage{endfloat}
-      - \setmainfont{Calibri}
+      # - \usepackage[UTF8, scheme=plain]{ctex}
-      - \usepackage[UTF8, scheme=plain]{ctex}
       - \usepackage{float}
       - \usepackage[normalem]{ulem}
       - \usepackage[doublespacing]{setspace}
       - \usepackage{lineno}
       - \linenumbers
-    journal:
-      formatting: preprint # preprint | review | doublebind
-      model: 1p
-      cite-style: authoryear
-      # graphical-abstract: "![](../figures/GA3.pdf)"
-      # highlights:
-      #   - A comprehensive model was contructed to evaluate the risk of odor occurrences
-      #   - Turbidity distribution determine underwater light and MIB-producing *Planktothrix*
-      #   - Increasing flowrate increases turbidity that can control *Planktothrix* and MIB
-      #   - Odor control based on flow regulation in source water is "green" and fundamental
 filters:
   - latex-environment
   - authors-block
 lightbox: auto
 commands: [clab]
+editor: 
+  markdown: 
+    wrap: sentence
 ---
 
 
@@ -75,7 +79,7 @@ require(lubridate)
 require(patchwork)
 require(drwateR)
 rmdify::rmd_init()
-biburl <- "http://drwater.rcees.ac.cn/cloud/s/ref_ming/download/Ref.bib"
+biburl <- "https://drc.drwater.net/datapool/public/BB/Ref.bib"
 if (!isRendering) { download.file(biburl, destfile = "Ref.bib") }
 ```
 

MS/SM.qmd

@@ -8,23 +8,32 @@ format:
     css: _extensions/inst/css/style.css
   docx:
     reference-doc: _extensions/inst/word/MS.docx
-  elsevier-pdf:
+  pdf:
-    classoption: [nopreprintline]
+    # documentclass: article
-    revision: true
+    latex-clean: false # to keep aux
-    keep-tex: true
+    citecolor: blue
-    latex-clean: false
+    colorlinks: true
-    include-in-header: "./_extensions/quarto-journals/elsevier/partials/revision.tex"
+    number-sections: false
+    sansfont: "Gill Sans"
+    papersize: a4paper
+    sansfontoptions: 
+      - Color=39729E
+    mainfont: "Source Sans 3" #| Verdana (fontsize: 11pt) # Source Sans 3 | Times New Roman| Helvetica | PT Sans
+    monofont: "JetBrains Mono"
+    mathfont: "Cambria Math"
+    CJKmainfont: SimHei
+    fontsize: 12pt
+    keep-md: false
+    include-in-header: "./_extensions/inst/tex/header.tex"
     header-includes:
+      - \let\oldsection\section
+      - \renewcommand{\section}{\clearpage\oldsection}
       # - \usepackage{threeparttable}
       # - \usepackage{fontspec}
-      # - \usepackage[nomarkers]{endfloat}
+      # - \usepackage{endfloat}
-      - \usepackage[normalem]{ulem}
+      # - \setmainfont{Calibri}
-      - \renewcommand{\thetable}{S\arabic{table}}
-      - \renewcommand{\thefigure}{S\arabic{figure}}
-      - \renewcommand{\theequation}{S\arabic{equation}}
-      - \setmainfont{Calibri}
       # - \usepackage[UTF8, scheme=plain]{ctex}
-      # - \usepackage{float}
+      - \usepackage{float}
       - \usepackage[normalem]{ulem}
       - \usepackage[doublespacing]{setspace}
       - \usepackage{lineno}
@@ -32,9 +41,11 @@ format:
 filters:
    - latex-environment
    - authors-block
+lightbox: auto
 commands: [clab]
 ---
 
+
 ```{r}
 #| label: setup
 #| include: false
@@ -47,7 +58,7 @@ require(lubridate)
 require(patchwork)
 require(drwateR)
 rmdify::rmd_init()
-biburl <- "http://drwater.rcees.ac.cn/datapool/public/BB/Ref.bib"
+biburl <- "https://drc.drwater.net/datapool/public/BB/Ref.bib"
 if (!isRendering) { download.file(biburl, destfile = "Ref.bib") }
 ```
 

_extensions/inst/tex/els.tex

@@ -284,7 +284,7 @@ $endif$
 \def\hascorr{0}
 \def\haseqc{0}
 % check if corresponding author(s) and equal contributing authors are available
-$for(author)$$if(author.correspondence)$\def\hascorr{1}$endif$$if(author.equalcontribution)$\def\haseqc{1}$endif$ $endfor$
+$for(author)$$if(author.correspondence)$\def\hascorr{1}$endif$$if(author.equal-contributor)$\def\haseqc{1}$endif$ $endfor$
 
 \newcommand{\getcorrauthinfo}{
     \subsection{Corresponding Author(s)}
@@ -361,7 +361,7 @@ $endfor$
 \begin{frontmatter}
 
    \title{$title$$if(subtitle)$\\\Large{$subtitle$}$endif$}
-   $for(author)$\author$if(authorwithinstitute)$[$for(author.institute)$$author.institute$$sep$,$endfor$]$endif${$author.name$$if(author.correspondence)$\corref{corrauth}$endif$$if(author.equalcontribution)$\corref{eqcon}$endif$ $if(author.footnote)$\fnref{$author.footnote$}$endif$}$if(author.email)$\ead{$author.email$}$endif$$endfor$
+   $for(author)$\author$if(authorwithinstitute)$[$for(author.institute)$$author.institute$$sep$,$endfor$]$endif${$author.name$$if(author.correspondence)$\corref{corrauth}$endif$$if(author.equal-contributor)$\corref{eqcon}$endif$ $if(author.footnote)$\fnref{$author.footnote$}$endif$}$if(author.email)$\ead{$author.email$}$endif$$endfor$
    $if(authorwithinstitute)$ $for(institute)$ \address[$institute.id$]{$institute.name$} $endfor$ $endif$
     % generate corresponding authors.
     % \StrBehind is from xstring package
@@ -373,7 +373,7 @@ $endfor$
 
     % generate equal contributing authors.
     \ifnum \haseqc=1
-        \def\eqa{$for(author)$$if(author.equalcontribution)$and $author.name$ $endif$$endfor$}
+        \def\eqa{$for(author)$$if(author.equal-contributor)$and $author.name$ $endif$$endfor$}
         \cortext[eqcon]{\StrBehind*{\eqa}{and } are equally contributed to this work.}
     \fi
 

_extensions/inst/tex/header.tex

@@ -0,0 +1,74 @@
+\usepackage{enumitem}
+\usepackage{fontspec}
+\usepackage{float}
+\usepackage[normalem]{ulem}
+\usepackage{hyperref}
+\usepackage{nameref} %needed by zref-xr
+\usepackage{zref-xr,zref-hyperref,zref-user}
+\usepackage{xr-hyper}
+
+
+\setkomafont{author}{\normalsize}
+
+\makeatletter
+\renewcommand{\title}[1]{\gdef\@title{\large\textbf{#1}}} % Adjust \Huge or other font commands
+% \renewcommand{\author}[1]{\gdef\@author{\normalsize\textrm{#1}}} % Adjust \Huge or other font commands
+% \renewcommand{\author}[1]{\normalsize\textit{#1}} % Use \normalsize and \textit for customization
+\makeatother
+
+\usepackage{adjustbox}
+% \usepackage{xcolor}
+\usepackage{mdframed}
+\newmdenv[topline=false,
+          leftline=true,
+          bottomline=false,
+          rightline=false,
+          linewidth=3pt,
+          %backgroundcolor=lightgray,
+          linecolor=gray!30,
+          backgroundcolor=gray!5,
+          skipabove=\topsep,
+          skipbelow=\topsep,
+          leftmargin=0pt,
+          rightmargin=0pt,
+          innertopmargin=0pt,
+          innerbottommargin=0pt
+          ]{refquote}
+\newmdenv[topline=false,
+          leftline=true,
+          bottomline=false,
+          rightline=false,
+          linewidth=3pt,
+          %backgroundcolor=lightgray,
+          backgroundcolor=red!3!white,
+          linecolor=red!30!white,
+          skipabove=\topsep,
+          skipbelow=\topsep,
+          leftmargin=0pt,
+          rightmargin=0pt,
+          innertopmargin=10pt,
+          innerbottommargin=10pt
+          ]{question}
+% setup hyperlink for page and line number
+\def\msname{MS}
+\def\smname{SM}
+\setenumerate{labelsep=*, leftmargin=1.0pc}
+%\zexternaldocument*{ManuscriptNew\veraa}
+\zexternaldocument*{\msname}
+\zexternaldocument*{\smname}
+\newcommand{\hlabel}[1]{\label{#1}\hypertarget{#1}{
+    \linelabel{line:#1}}}
+%\externaldocument[si-]{\smname\veraa}[\smname\veraa.pdf]
+\makeatletter
+\newcommand{\clab}[2][]{
+		\protected@write\@auxout{\let\clab\@secondoftwo}{
+				\string\newlabel{r:#1}{{#2}{}}}%
+		\hlabel{#1}#2\hlabel{#1end}}
+\makeatother 
+\newcommand{\zhypera}[1]{\href[pdfnewwindow]{\msname.pdf\##1}{\\[1ex]\textbf{Page \zpageref{#1}, Line
+\zref{line:#1}--\zref{line:#1end}:}\\}}
+\newcommand{\cref}[1]{\begin{refquote}\zhypera{#1}{\zref{r:#1}}\\[-0.5ex]\end{refquote}}
+% \newenvironment{ra}[1][\unskip]{\par \noindent \\[-1ex] \textbf{Response/Action:}\par\bf}{\ \\}
+\renewenvironment{quote}{\begin{question}}{\end{question}}
+% \renewenvironment{verbatim}{\begin{ra}}{\end{ra}}
+

_extensions/kapsner/authors-block/from_author_info_blocks.lua

@@ -19,25 +19,21 @@ THIS SOFTWARE.
 
 -- from @kapsner
 -- [import]
-local from_utils = require "utils"
+local from_utils = require("utils")
 local has_key = from_utils.has_key
 -- [/import]
 local M = {}
 
 -- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
-local List = require 'pandoc.List'
+local List = require("pandoc.List")
-local utils = require 'pandoc.utils'
+local utils = require("pandoc.utils")
 local stringify = utils.stringify
 
 -- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
 local default_marks
 local default_marks = {
-  corresponding_author = FORMAT == 'latex'
+	corresponding_author = FORMAT == "latex" and { pandoc.RawInline("latex", "*") } or { pandoc.Str("✉") },
-    and {pandoc.RawInline('latex', '*')}
+	equal_contributor = FORMAT == "latex" and { pandoc.RawInline("latex", "†") } or { pandoc.Str("†") },
-    or {pandoc.Str '✉'},
-  equal_contributor = FORMAT == 'latex'
-    and {pandoc.RawInline('latex', '$\\dagger{}$')}
-    or {pandoc.Str '*'},
 }
 M.default_marks = default_marks
 
@@ -58,18 +54,17 @@ local function create_equal_contributors_block(authors, mark)
 		return nil
 	end
 	local contributors = {
-    pandoc.Superscript(mark'equal_contributor'),
+		pandoc.Superscript(mark("equal_contributor")),
 		pandoc.Space(),
-    pandoc.Str 'These authors contributed equally to this work.'
+		pandoc.Str("These authors contributed equally to this work."),
 	}
-  return List:new{pandoc.Para(contributors)}
+	return List:new({ pandoc.Para(contributors) })
 end
 M.create_equal_contributors_block = create_equal_contributors_block
 
-
 -- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
 local function intercalate(lists, elem)
-  local result = List:new{}
+	local result = List:new({})
 	for i = 1, (#lists - 1) do
 		result:extend(lists[i])
 		result:extend(elem)
@@ -95,65 +90,68 @@ M.is_corresponding_author = is_corresponding_author
 -- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
 --- Generate a block element containing the correspondence information
 local function create_correspondence_blocks(authors, mark)
-  local corresponding_authors = List:new{}
+	local corresponding_authors = List:new({})
 	for _, author in ipairs(authors) do
 		if is_corresponding_author(author) then
-      local mailto = 'mailto:' .. utils.stringify(author.email)
+			local mailto = "mailto:" .. utils.stringify(author.email)
 			local author_with_mail = List:new(
 				-- modified by @kapsner
-        author.name.literal .. List:new{pandoc.Space(),  pandoc.Str '<'} ..
+				author.name.literal
-        author.email .. List:new{pandoc.Str '>'}
+					.. List:new({ pandoc.Space(), pandoc.Str("<") })
+					.. author.email
+					.. List:new({ pandoc.Str(">") })
 			)
 			local link = pandoc.Link(author_with_mail, mailto)
-      table.insert(corresponding_authors, {link})
+			table.insert(corresponding_authors, { link })
 		end
 	end
 	if #corresponding_authors == 0 then
 		return nil
 	end
-  local correspondence = List:new{
+	local correspondence = List:new({
-    pandoc.Superscript(mark'corresponding_author'),
+		pandoc.Superscript(mark("corresponding_author")),
 		pandoc.Space(),
-    pandoc.Str'Correspondence:',
+		pandoc.Str("Correspondence:"),
-    pandoc.Space()
+		pandoc.Space(),
-  }
+	})
-  local sep = List:new{pandoc.Str',',  pandoc.Space()}
+	local sep = List:new({ pandoc.Str(","), pandoc.Space() })
 	return {
-    pandoc.Para(correspondence .. intercalate(corresponding_authors, sep))
+		pandoc.Para(correspondence .. intercalate(corresponding_authors, sep)),
 	}
 end
 M.create_correspondence_blocks = create_correspondence_blocks
 
 -- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
 --- Create inlines for a single author (includes all author notes)
-local function author_inline_generator (get_mark)
+local function author_inline_generator(get_mark)
-  return function (author)
+	return function(author)
-    local author_marks = List:new{}
+		local author_marks = List:new({})
 		-- modified by @kapsner
 		if has_key(author, "attributes") then
 			if author.attributes["equal-contributor"] then
-        author_marks[#author_marks + 1] = get_mark 'equal_contributor'
+				author_marks[#author_marks + 1] = get_mark("equal_contributor")
 			end
 		end
 		local idx_str
 		for _, idx in ipairs(author.affiliations) do
-      if type(idx) ~= 'table' then
+			if type(idx) ~= "table" then
 				idx_str = tostring(idx)
 			else
 				idx_str = stringify(idx)
 			end
-      author_marks[#author_marks + 1] = {pandoc.Str(idx_str)}
+			author_marks[#author_marks + 1] = { pandoc.Str(idx_str) }
 		end
 		if is_corresponding_author(author) then
-      author_marks[#author_marks + 1] = get_mark 'corresponding_author'
+			author_marks[#author_marks + 1] = get_mark("corresponding_author")
 		end
 		-- modified by @kapsner
-    if FORMAT:match 'latex' then
+		if FORMAT:match("latex") then
-      author.name.literal[#author.name.literal + 1] = pandoc.Superscript(intercalate(author_marks, {pandoc.Str ','}))
+			author.name.literal[#author.name.literal + 1] =
+				pandoc.Superscript(intercalate(author_marks, { pandoc.Str(",") }))
 			return author
 		else
 			local res = List.clone(author.name.literal)
-      res[#res + 1] = pandoc.Superscript(intercalate(author_marks, {pandoc.Str ','}))
+			res[#res + 1] = pandoc.Superscript(intercalate(author_marks, { pandoc.Str(",") }))
 			return res
 		end
 	end
@@ -165,13 +163,13 @@ M.author_inline_generator = author_inline_generator
 local function create_authors_inlines(authors, mark)
 	local inlines_generator = author_inline_generator(mark)
 	local inlines = List:new(authors):map(inlines_generator)
-  local and_str = List:new{pandoc.Space(), pandoc.Str'and', pandoc.Space()}
+	local and_str = List:new({ pandoc.Space(), pandoc.Str("and"), pandoc.Space() })
 
 	local last_author = inlines[#inlines]
 	inlines[#inlines] = nil
-  local result = intercalate(inlines, {pandoc.Str ',', pandoc.Space()})
+	local result = intercalate(inlines, { pandoc.Str(","), pandoc.Space() })
 	if #authors > 1 then
-    result:extend(List:new{pandoc.Str ","} .. and_str)
+		result:extend(List:new({ pandoc.Str(",") }) .. and_str)
 	end
 	result:extend(last_author)
 	return result
@@ -181,16 +179,14 @@ M.create_authors_inlines = create_authors_inlines
 -- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
 --- Generate a block list all affiliations, marked with arabic numbers.
 local function create_affiliations_blocks(affiliations)
-  local affil_lines = List:new(affiliations):map(
+	local affil_lines = List:new(affiliations):map(function(affil, i)
-    function (affil, i)
+		local num_inlines = List:new({
-      local num_inlines = List:new{
+			pandoc.Superscript({ pandoc.Str(affil.number) }),
-        pandoc.Superscript{pandoc.Str(affil.number)},
+			pandoc.Space(),
-        pandoc.Space()
+		})
-      }
 		return num_inlines .. affil.name
-    end
+	end)
-  )
+	return { pandoc.Para(intercalate(affil_lines, { pandoc.LineBreak() })) }
-  return {pandoc.Para(intercalate(affil_lines, {pandoc.LineBreak()}))}
 end
 M.create_affiliations_blocks = create_affiliations_blocks
 

_extensions/quarto-journals/elsevier/partials/revision.tex

@@ -7,6 +7,11 @@
 \usepackage{zref-xr,zref-hyperref,zref-user}
 \usepackage{xr-hyper}
 
+\makeatletter
+\renewcommand{\title}[1]{\gdef\@title{\Large\textbf{#1}}} % Adjust \Huge or other font commands
+% \renewcommand{\author}[1]{\gdef\@author{\normalsize\textrm{#1}}} % Adjust \Huge or other font commands
+% \renewcommand{\author}[1]{\normalsize\textit{#1}} % Use \normalsize and \textit for customization
+\makeatother
 
 \usepackage{adjustbox}
 % \usepackage{xcolor}

_quarto.yml

@@ -8,7 +8,7 @@ author:
   - name: Ming Su
     email: mingsu@rcees.ac.cn
     orcid: 0000-0001-9821-1268
-    url: https://drwater.rcees.ac.cn
+    url: https://drwater.net/team/ming-su/
     affiliations:
       - ref: skleac
       - ref: ucas
@@ -110,11 +110,11 @@ project:
 website:
   title: "Version: {{< var branch >}}"
   reader-mode: true
-  site-url: https://drwater.rcees.ac.cn/{{< var pubtype >}}/{{< var projtype >}}/{{< var reponame >}}/@{{< var branch >}}
+  site-url: https://drc.drwater.net/{{< var pubtype >}}/{{< var projtype >}}/{{< var reponame >}}/{{< var branch >}}
-  repo-url: https://drwater.rcees.ac.cn/git/{{< var projtype >}}/{{< var reponame >}}
+  repo-url: https://git.drwater.net/{{< var projtype >}}/{{< var reponame >}}
   repo-actions: [edit, source, issue]
   page-navigation: true
-  page-footer: "Copyright 2023, [Ming Su](https://drwater.rcees.ac.cn)"
+  page-footer: "Copyright 2024, [Dr. Water](https://drwater.net)"
   navbar:
     background: "grey"
     search: true
@@ -145,9 +145,9 @@ website:
       - icon: git
         menu:
           - text: Edit
-            url: https://drwater.rcees.ac.cn/git/{{< var projtype >}}/{{< var reponame >}}/src/branch/{{< var branch >}}
+            url: https://git.drwater.net/{{< var projtype >}}/{{< var reponame >}}/src/branch/{{< var branch >}}
           - text: Issue
-            url: https://drwater.rcees.ac.cn/git/manuscript/{{< var reponame >}}/issues
+            url: https://git.drwater.net/manuscript/{{< var reponame >}}/issues
   comments:
     hypothesis:
       theme: clean